Abstract: Continuous cropping of soybean (Glycine max) in north China is an increasingly prominent problem and attracting widespread attention. Arbuscular mycorrhizal fungi (AMF) are applied in continuous cropping soil in order to reduce continuous cropping obstacles. In this study, Nested-PCR-DGGE technology was used to analyze the effect of Funneliformis mosseae on community structure of AMF in three different continuous cropping soils for three soybean varieties at seedling stage. The results indicated that the infection rate of AMF was the highest in the same soybean variety with two continuous cropping years after inoculating F. mosseae. The colonization rate of AMF was the maximum in KF16 in the same continuous cropping year. There were Glomus viscosum and Uncultured Glomus in the soybean varieties’roots at different continuous cropping years. The abundance value and Shannon-Wiener index of AMF of soybean roots with two continuous cropping years were higher than those with zero continuous cropping year and one continuous cropping year. It revealed that F. mosseae significantly influenced the community structure of AMF in different soybean varieties’roots of one continuous cropping year and two continuous cropping years at seedling stage.